detection-and-isolation-of-campylobacter-spp-from-raw-meat

Detection and Isolation of <i>Campylobacter </i> spp. from Raw Meat 

This article presents a rapid yet robust protocol for isolating Campylobacter spp. from raw meats, specifically focusing on Campylobacter jejuni and ...

modified-most-probable-number-assay-to-quantify-salmonella-raw-ready

Modified Most Probable Number Assay to Quantify <em>Salmonella</em> in Raw and Ready-to-Cook Chicken Products

Salmonella is a leading cause of foodborne illness in the United States, particularly in poultry products. Traditional methods for detecting Salmonella ...

Agricultural Research Service (ARS), United States Department of Agriculture (USDA)

Shiga toxin-producing  (STEC) and  are routinely responsible for severe foodborne illnesses in the United States. Current identification methods utilized by the U.S. Food Safety Inspection Service require at least four days to identify STEC and six days for . Adoption of long-read, whole genome sequencing for food safety testing could significantly reduce the time needed for identification, but method development costs are high. Therefore, the goal of this project was to use NanoSim-H software to simulate Oxford Nanopore sequencing reads to assess the feasibility of sequencing-based foodborne pathogen detection and guide experimental design. Sequencing reads were simulated for STEC, , and a 1:1 combination of STEC and  genomes using NanoSim-H. At least 2500 simulated reads were needed to identify the seven genes of interest targeted in STEC, and at least 500 reads were needed to detect the gene targeted in . Genome coverage of 30x was estimated at 21,521, and 11,802 reads for STEC and , respectively. Approximately 5-6% of reads simulated from both bacteria did not align with their respective reference genomes due to the introduction of errors. For the STEC and  1:1 genome mixture, all genes of interest were detected with 1,000,000 reads, but less than 1x coverage was obtained. The results suggested sample enrichment would be necessary to detect foodborne pathogens with long-read sequencing, but this would still decrease the time needed from current methods. Additionally, simulation data will be useful for reducing the time and expense associated with laboratory experimentation.

Evaluation of Long-Read Sequencing Simulators to Assess Real-World Applications for Food Safety.

 is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of  infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43  and  strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., (3')-III, type IV and VI secretion systems, and type II toxin-antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of . Together, the identification and comprehensive genetic characterization of new plasmids from  food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen.

Katrina Counihan

Agricultural Research Service (ARS), United States Department of Agriculture (USDA)

Detection and Isolation of Campylobacter spp. from Raw Meat

Modified Most Probable Number Assay to Quantify Salmonella in Raw and Ready-to-Cook Chicken Products